-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_10294867-10617333

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for Augustus_model.g33447.t1
Valid prediction for GlimmerHMM_glimmerT_50137-T1
Valid prediction for GlimmerHMM_glimmerT_50126-T1
Valid prediction for snap_scaffold_22-snap.2135-T1
Valid prediction for snap_scaffold_22-snap.2133-T1
Valid prediction for GlimmerHMM_glimmerT_50149-T1
Valid prediction for GlimmerHMM_glimmerT_50125-T1
Valid prediction for GlimmerHMM_glimmerT_50132-T1
Valid prediction for snap_scaffold_22-snap.2120-T1
Valid prediction for GlimmerHMM_glimmerT_50124-T1
Valid prediction for snap_scaffold_22-snap.2140-T1
Couldn't classify 227368, 227399
Couldn't classify 228905, 228984
Sorry, prediction pasa_asmbl_30358.p1 fails validation.
(GCC)	 TA	227368-227399	GT	GGG
(TGG)	 AG	227730-227814	GT	GGG
(CTG)	 AG	228255-228353	GT	TGG
(GGG)	 AG	228441-228582	GT	CGG
(GAG)	 AG	228905-228984	TG	GCT
-recovered pasa_asmbl_30358.p1, internal, 227730, 227814
-recovered pasa_asmbl_30358.p1, internal, 228255, 228353
-recovered pasa_asmbl_30358.p1, internal, 228441, 228582
Valid prediction for Augustus_model.g33449.t1
Valid prediction for snap_scaffold_22-snap.2146-T1
Valid prediction for Augustus_model.g33442.t1
Valid prediction for GlimmerHMM_glimmerT_50143-T1
Valid prediction for snap_scaffold_22-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_50146-T1
Valid prediction for snap_scaffold_22-snap.2112-T1
Valid prediction for Augustus_model.g33445.t1
Couldn't classify 48721, 48757
Couldn't classify 50067, 50149
Sorry, prediction pasa_asmbl_30472.p1 fails validation.
(TCT)	 GA	48721-48757	GT	AGG
(GGT)	 AG	49079-49371	GT	AGG
(CTA)	 AG	49707-49785	GT	TGG
(GTA)	 AG	50067-50149	GG	TGG
-recovered pasa_asmbl_30472.p1, internal, 49079, 49371
-recovered pasa_asmbl_30472.p1, internal, 49707, 49785
Valid prediction for Augustus_model.g33456.t1
Valid prediction for Augustus_model.g33448.t1
Valid prediction for snap_scaffold_22-snap.2128-T1
Valid prediction for snap_scaffold_22-snap.2126-T1
Couldn't classify 51879, 51969
Couldn't classify 53151, 53248
Sorry, prediction pasa_asmbl_30513.p1 fails validation.
(GGT)	 CA	51879-51969	GT	AGG
(AGG)	 AG	52047-52163	GT	TGG
(ATG)	 AG	52474-52593	GT	AGG
(GTC)	 AG	52900-53037	GT	AGG
(CCA)	 AG	53151-53248	AT	CTA
add_exon() Sorry, pasa_asmbl_30513.p1 52474-52593-initial-1 is invalid.
-recovered pasa_asmbl_30513.p1, initial, 52474, 52593
-recovered pasa_asmbl_30513.p1, internal, 52047, 52163
-recovered pasa_asmbl_30513.p1, internal, 52474, 52593
-recovered pasa_asmbl_30513.p1, internal, 52900, 53037
Valid prediction for GlimmerHMM_glimmerT_50129-T1
Valid prediction for Augustus_model.g33454.t1
Valid prediction for GlimmerHMM_glimmerT_50145-T1
Valid prediction for snap_scaffold_22-snap.2111-T1
Valid prediction for Augustus_model.g33446.t1
Valid prediction for GlimmerHMM_glimmerT_50147-T1
Valid prediction for Augustus_model.g33453.t1
Valid prediction for snap_scaffold_22-snap.2124-T1
Valid prediction for snap_scaffold_22-snap.2134-T1
Valid prediction for snap_scaffold_22-snap.2138-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.2148-T1
Valid prediction for snap_scaffold_22-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_50130-T1
Valid prediction for snap_scaffold_22-snap.2118-T1
Valid prediction for snap_scaffold_22-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_50131-T1
Valid prediction for snap_scaffold_22-snap.2143-T1
Valid prediction for snap_scaffold_22-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_50121-T1
Couldn't classify 65757, 65836
Couldn't classify 66089, 66200
Couldn't classify 70186, 70280
Couldn't classify 71102, 71139
Sorry, prediction CodingQuarry_transcript_34273-T1 fails validation.
(ATG)	 TG	64537-64598	GT	CAG
(GTT)	 AG	65261-65449	GT	GGG
(AGT)	 AG	65757-65836	CG	GGC
(CCC)	 TC	66089-66200	GT	GTG
(GTA)	 AG	67961-68073	GT	GGG
(AGT)	 AG	68378-68489	GT	AGG
(CTG)	 AG	69400-69540	GT	AAG
(TGA)	 AG	70186-70280	AG	GGA
(AGG)	 CC	71102-71139	GT	CTG
(CTC)	 AG	71499-71597	GA	GAG
-recovered CodingQuarry_transcript_34273-T1, initial, 64537, 64598
-recovered CodingQuarry_transcript_34273-T1, terminal, 71499, 71597
-recovered CodingQuarry_transcript_34273-T1, internal, 65261, 65449
-recovered CodingQuarry_transcript_34273-T1, internal, 67961, 68073
-recovered CodingQuarry_transcript_34273-T1, internal, 68378, 68489
-recovered CodingQuarry_transcript_34273-T1, internal, 69400, 69540
Valid prediction for GlimmerHMM_glimmerT_50119-T1
Valid prediction for snap_scaffold_22-snap.2109-T1
Valid prediction for snap_scaffold_22-snap.2156-T1
Valid prediction for GlimmerHMM_glimmerT_50139-T1
Valid prediction for GlimmerHMM_glimmerT_50138-T1
Valid prediction for snap_scaffold_22-snap.2153-T1
Valid prediction for snap_scaffold_22-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_50128-T1
Valid prediction for GlimmerHMM_glimmerT_50148-T1
Valid prediction for snap_scaffold_22-snap.2125-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_22-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_50142-T1
Valid prediction for GlimmerHMM_glimmerT_50135-T1
Valid prediction for Augustus_model.g33444.t1
Valid prediction for Augustus_model.g33443.t1
Valid prediction for GlimmerHMM_glimmerT_50123-T1
Valid prediction for GlimmerHMM_glimmerT_50136-T1
Valid prediction for GlimmerHMM_glimmerT_50150-T1
Valid prediction for snap_scaffold_22-snap.2117-T1
Valid prediction for snap_scaffold_22-snap.2145-T1
Couldn't classify 223754, 223834
Sorry, prediction pasa_asmbl_29602.p1 fails validation.
(ATG)	 TA	222120-222260	GT	AGG
(GCC)	 AG	222632-222761	GT	CGG
(GAC)	 AG	223034-223137	GT	AGG
(GGG)	 AG	223302-223403	GT	AGG
(GTT)	 AG	223754-223834	GT	TGG
-recovered pasa_asmbl_29602.p1, initial, 222120, 222260
-recovered pasa_asmbl_29602.p1, internal, 222632, 222761
-recovered pasa_asmbl_29602.p1, internal, 223034, 223137
-recovered pasa_asmbl_29602.p1, internal, 223302, 223403
-recovered pasa_asmbl_29602.p1, internal, 223754, 223834
Valid prediction for snap_scaffold_22-snap.2122-T1
Valid prediction for snap_scaffold_22-snap.2130-T1
Valid prediction for HiQ_model.g33450.t1
Valid prediction for snap_scaffold_22-snap.2147-T1
Valid prediction for snap_scaffold_22-snap.2115-T1
Valid prediction for snap_scaffold_22-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_50122-T1
Valid prediction for snap_scaffold_22-snap.2113-T1
Valid prediction for snap_scaffold_22-snap.2141-T1
Valid prediction for snap_scaffold_22-snap.2129-T1
Valid prediction for snap_scaffold_22-snap.2139-T1
Valid prediction for GlimmerHMM_glimmerT_50120-T1
Valid prediction for GlimmerHMM_glimmerT_50127-T1
Valid prediction for GlimmerHMM_glimmerT_50152-T1
Valid prediction for snap_scaffold_22-snap.2110-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g33455.t1
Valid prediction for snap_scaffold_22-snap.2137-T1
Valid prediction for snap_scaffold_22-snap.2155-T1
Valid prediction for snap_scaffold_22-snap.2114-T1
Valid prediction for snap_scaffold_22-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_50151-T1
Valid prediction for snap_scaffold_22-snap.2151-T1
Valid prediction for GlimmerHMM_glimmerT_50133-T1
Valid prediction for GlimmerHMM_glimmerT_50144-T1
Valid prediction for snap_scaffold_22-snap.2123-T1
Valid prediction for snap_scaffold_22-snap.2127-T1
Couldn't classify 191041, 191187
Couldn't classify 194533, 194552
Sorry, prediction pasa_asmbl_29603.p1 fails validation.
(GAG)	 CA	191041-191187	GT	AGG
(TCT)	 AG	191940-192118	GT	TGG
(GGA)	 AG	192784-192925	GT	AGG
(TGT)	 AG	193672-193891	GT	GGG
(ACC)	 AG	194533-194552	GT	GGG
-recovered pasa_asmbl_29603.p1, internal, 191940, 192118
-recovered pasa_asmbl_29603.p1, internal, 192784, 192925
-recovered pasa_asmbl_29603.p1, internal, 193672, 193891
-recovered pasa_asmbl_29603.p1, internal, 194533, 194552
Valid prediction for snap_scaffold_22-snap.2152-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g33451.t1
Valid prediction for Augustus_model.g33458.t1
Valid prediction for snap_scaffold_22-snap.2142-T1
Valid prediction for GlimmerHMM_glimmerT_50134-T1
Valid prediction for Augustus_model.g33452.t1
Couldn't classify 110479, 111165
Sorry, prediction pasa_asmbl_29605.p1 fails validation.
(TCC)	 AC	110479-111165	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_50141-T1
Valid prediction for Augustus_model.g33457.t1
Valid prediction for GlimmerHMM_glimmerT_50140-T1
Valid prediction for snap_scaffold_22-snap.2121-T1
Valid prediction for snap_scaffold_22-snap.2132-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15612, rend_intergenic: 6904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33862, rend_intergenic: 16267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45388, rend_intergenic: 33957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50442, rend_intergenic: 47781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53154, rend_intergenic: 50651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53281, rend_intergenic: 53173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57114, rend_intergenic: 54064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83764, rend_intergenic: 57364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94316, rend_intergenic: 84051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95923, rend_intergenic: 94948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119870, rend_intergenic: 101670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132214, rend_intergenic: 125973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147937, rend_intergenic: 132305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171543, rend_intergenic: 148061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178200, rend_intergenic: 175081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178847, rend_intergenic: 178223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192697, rend_intergenic: 178975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204973, rend_intergenic: 193109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212972, rend_intergenic: 205608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226833, rend_intergenic: 226239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232246, rend_intergenic: 227371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251748, rend_intergenic: 234887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306459, rend_intergenic: 251760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 313725, rend_intergenic: 307177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 321287, rend_intergenic: 314655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 322467
-exon list size: 465


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15612, rend_intergenic: 6904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33862, rend_intergenic: 16267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45388, rend_intergenic: 33957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50442, rend_intergenic: 47781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53154, rend_intergenic: 50651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53281, rend_intergenic: 53173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57114, rend_intergenic: 54064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83764, rend_intergenic: 57364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94316, rend_intergenic: 84051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95923, rend_intergenic: 94948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119870, rend_intergenic: 101670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132214, rend_intergenic: 125973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147937, rend_intergenic: 132305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171543, rend_intergenic: 148061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178200, rend_intergenic: 175081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178847, rend_intergenic: 178223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192697, rend_intergenic: 178975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204973, rend_intergenic: 193109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212972, rend_intergenic: 205608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226833, rend_intergenic: 226239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232246, rend_intergenic: 227371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251748, rend_intergenic: 234887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306459, rend_intergenic: 251760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 313725, rend_intergenic: 307177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 321287, rend_intergenic: 314655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support